PDB entry 7k8x

View 7k8x on RCSB PDB site
Description: structure of the sars-cov-2 s 2p trimer in complex with the human neutralizing antibody fab fragment, c121 (state 1)
Deposited on 2020-09-27, released 2020-10-21
The last revision was dated 2021-01-13, with a file datestamp of 2021-01-08.
Experiment type: EM
Resolution: 3.9 Å
R-factor: N/A
AEROSPACI score: 0.12 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2
      • conflict (985-986)
  • Chain 'B':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2
      • conflict (985-986)
  • Chain 'C':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2
      • conflict (985-986)
  • Chain 'D':
    Compound: C121 Fab Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K8X (0-End)
  • Chain 'E':
    Compound: C121 Fab Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K8X (0-End)
  • Chain 'F':
    Compound: C121 Fab Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K8X
  • Chain 'G':
    Compound: C121 Fab Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K8X
  • Heterogens: NAG

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >7k8xA (A:)
mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
ecdipigagicasyqtqtnsprrarsvasqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
qelgkyeqyikwpsgrlvprgspgsgyipeaprdgqayvrkdgewvllstflghhhhhh

    Sequence, based on observed residues (ATOM records):
    >7k8xA (A:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihdnpvlpfndgvyfaste
ksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfknlr
efvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhaayyv
gylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesiv
rfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptkl
ndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvgg
nynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqp
yrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgr
diadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtra
gcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnft
isvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntq
evfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppll
tdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklian
qfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrld
ppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgk
gyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvt
qrnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'B':
    Sequence, based on SEQRES records:
    >7k8xB (B:)
mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
ecdipigagicasyqtqtnsprrarsvasqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
qelgkyeqyikwpsgrlvprgspgsgyipeaprdgqayvrkdgewvllstflghhhhhh

    Sequence, based on observed residues (ATOM records):
    >7k8xB (B:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihdnpvlpfndgvyfaste
ksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfknlr
efvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhaayyv
gylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesiv
rfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptkl
ndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvgg
nynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqp
yrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgr
diadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtra
gcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnft
isvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntq
evfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppll
tdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklian
qfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrld
ppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgk
gyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvt
qrnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'C':
    Sequence, based on SEQRES records:
    >7k8xC (C:)
mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
ecdipigagicasyqtqtnsprrarsvasqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
qelgkyeqyikwpsgrlvprgspgsgyipeaprdgqayvrkdgewvllstflghhhhhh

    Sequence, based on observed residues (ATOM records):
    >7k8xC (C:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihdnpvlpfndgvyfaste
ksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfknlr
efvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhaayyv
gylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesiv
rfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptkl
ndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvgg
nynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqp
yrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgr
diadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtra
gcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnft
isvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntq
evfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppll
tdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklian
qfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrld
ppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgk
gyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvt
qrnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'D':
    Sequence, based on SEQRES records:
    >7k8xD (D:)
qvqlvqsgaevkkpgasvkvsckasgytftgyymhwvrqapgqglewmgwispvsggtny
aqkfqgrvtmtrdtsistaymelsrlrsddtavyycaraplfptgvlagdyyyygmdvwg
qgttvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvh
tfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdkthhhhh
h

    Sequence, based on observed residues (ATOM records):
    >7k8xD (D:)
qvqlvqsgaevkkpgasvkvsckasgytftgyymhwvrqapgqglewmgwispvsggtny
aqkfqgrvtmtrdtsistaymelsrlrsddtavyycaraplfptgvlagdyyyygmdvwg
qgttvtvs

  • Chain 'E':
    Sequence, based on SEQRES records:
    >7k8xE (E:)
qvqlvqsgaevkkpgasvkvsckasgytftgyymhwvrqapgqglewmgwispvsggtny
aqkfqgrvtmtrdtsistaymelsrlrsddtavyycaraplfptgvlagdyyyygmdvwg
qgttvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvh
tfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdkthhhhh
h

    Sequence, based on observed residues (ATOM records):
    >7k8xE (E:)
qvqlvqsgaevkkpgasvkvsckasgytftgyymhwvrqapgqglewmgwispvsggtny
aqkfqgrvtmtrdtsistaymelsrlrsddtavyycaraplfptgvlagdyyyygmdvwg
qgttvtvs

  • Chain 'F':
    Sequence, based on SEQRES records:
    >7k8xF (F:)
qsaltqpasvsgspgqsitisctgtssdvgsynlvswyqqhpgkapklmiyegskrpsgv
snrfsgsksgntasltisglqaedeadyyccsyagsstlvfgggtkltvlgqpkaapsvt
lfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaass
ylsltpeqwkshrsyscqvthegstvektvaptecs

    Sequence, based on observed residues (ATOM records):
    >7k8xF (F:)
altqpasvsgspgqsitisctgtssdvgsynlvswyqqhpgkapklmiyegskrpsgvsn
rfsgsksgntasltisglqaedeadyyccsyagsstlvfgggtkltvl

  • Chain 'G':
    Sequence, based on SEQRES records:
    >7k8xG (G:)
qsaltqpasvsgspgqsitisctgtssdvgsynlvswyqqhpgkapklmiyegskrpsgv
snrfsgsksgntasltisglqaedeadyyccsyagsstlvfgggtkltvlgqpkaapsvt
lfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaass
ylsltpeqwkshrsyscqvthegstvektvaptecs

    Sequence, based on observed residues (ATOM records):
    >7k8xG (G:)
altqpasvsgspgqsitisctgtssdvgsynlvswyqqhpgkapklmiyegskrpsgvsn
rfsgsksgntasltisglqaedeadyyccsyagsstlvfgggtkltvl